Disorders of mitochondrial (FAO) are among the most frequent identified through newborn screening in the US. FAO is traditionally viewed as an energy-generating, catabolic pathway but intermediates of this pathway can serve as key substrates for synthesis of other complex lipids. The long range objective of this project is to define the role of FAO proteins in intermediary metabolism and the clinical impact of their deficiency due to inborn errors. Progress made on these aims has provided revolutionary insight into the molecular architecture of mitochondrial energy metabolism and positions us to leverage this knowledge for the development of novel therapies for long chain fatty acid oxidation disorders. The overall goal of this renewal application is to use integrative biology to characterize the molecular architecture of mitochondrial energy metabolism and to understand the global metabolic defects induced by deficiency of single enzyme disorders. Specific Aim 1 is to identify the key protein interactions that stabilize the macromolecular mitochondrial energy complex. I will examine the interactions of three specific sets of proteins based on my previous findings Specific Aim 1a is to use proteomics techniques to examine amino acid residues critical to the formation and stability of the proteins of long chain FAO. Specific Aim 1b is to directly examine the three dimensional structure of the multifunctional energy complex. Specific Aim 2 is to examine the effects of mutations in long chain FAO proteins on the macromolecular mitochondrial energy complex. I hypothesize that some mutations will not only inactivate the mutated protein, but also disrupt the stability and function of the macromolecular mitochondrial energy complex Specific Aim 2a is to examine the effects of patient and CRISPR/Cas9 induced mutations in cell lines and an FAOD mouse model on interaction of the long chain FAO complex core proteins with their binding partners.. Specific Aim 2b is to examine the effects of mutations in ETFDH on its interaction with complex III. Specific Specific Aim 2c is to characterize new mutations in patients with FAODs. Aim 3 is to develop novel small molecule compounds to treat long chain FAODs. I have previously used molecular modeling and an in vitro cell system to identify potential therapeutic small molecule chaperonins and peptides that stabilizes the common Glu304Lys mutant MCAD protein, one of which is currently in clinical trials in patients. My collaborators and I have also shown that some ACAD9 mutations are stabilized by supplementation with excess riboflavin, similar to a finding with some ETFDH mutations. I hypothesize that additional therapeutic molecules have the potential to stabilize other mutant fatty acid oxidation proteins and mitigate the atypical inflammatory process seen in VLCAD deficiency. Specific Aim 3a is to examine the use of novel pharmaceutical agents known to affect energy metabolism and inflammation in cells from patients with FAODs. Specific Aim 3b is to examine the effect of these compounds in mouse models of FAODs in order to prepare for possible clinical trials in patients.